3EN7

Targeted polypharmacology: crystal structure of the c-Src kinase domain in complex with S1, a multitargeted kinase inhibitor


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829816 mg/mL kinase, 50 mM Tris-HCl, 100 mM NaCl, 5% (v/v) glycerol mixed 1:1 with 18% (w/v) glycerol precipitant well solution, pH 8.0, vapor diffusion, hanging drop, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.9758.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.429α = 100.84
b = 62.984β = 91.81
c = 74.028γ = 89.61
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152007-07-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.21.000ALS8.2.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.85098.80.12411.7633.818046
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.82.998.20.4973.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.8137.131710292498.40.209210.206610.2574RANDOM14.27
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
-0.03-0.010.020.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.216
r_dihedral_angle_4_deg17.313
r_dihedral_angle_3_deg16.467
r_dihedral_angle_1_deg6.325
r_scangle_it2.828
r_scbond_it1.714
r_angle_refined_deg1.538
r_mcangle_it0.931
r_mcbond_it0.477
r_nbtor_refined0.301
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.216
r_dihedral_angle_4_deg17.313
r_dihedral_angle_3_deg16.467
r_dihedral_angle_1_deg6.325
r_scangle_it2.828
r_scbond_it1.714
r_angle_refined_deg1.538
r_mcangle_it0.931
r_mcbond_it0.477
r_nbtor_refined0.301
r_symmetry_vdw_refined0.196
r_nbd_refined0.192
r_xyhbond_nbd_refined0.131
r_symmetry_hbond_refined0.131
r_chiral_restr0.092
r_bond_refined_d0.013
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3774
Nucleic Acid Atoms
Solvent Atoms6
Heterogen Atoms20

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling